Introduction

TopoStats is a Python package that aims to simplify batch processing Atomic Force Microscopy (AFM) images.

Input directories are recursively searched for files of a given type. Each image is then loaded and processed. Multiple images can be processed in parallel.

Once an image has been loaded the specified channel of data extracted along with the pixel to nanometre scaling. This data is then aligned and the tilt is removed. Configurable thresholds are then used to generate masks and a second round of tilt removal and row alignment is performed.

Molecules/regions of interest known as Grains are then detected based on user specified thresholds and the detected regions are labelled and have preliminary statistics calculated. The labelled regions of each grain then have individual statistics calculated capturing the height, volume, radius and the location of the centroid.

Optionally DNA Tracing is then performed, which traces the backbone of the DNA molecules to calculate further statistics such as whether grains are linear or circular, their contour length and end-to-end distances etc.

The resulting statistics are written to a CSV file and optionally plots are then generated from various stages of the processing as well as cropped images of each grain. The amount of images produced is also configurable.

An schematic overview of the classes and methods that are run in processing files can be found in the workflow page along with more detailed information on installation, usage, configuration and contributing.

If you have questions, please post them on the discussion, if you think you’ve encountered a bug whilst running the code or suggestions for improvements please create an issue in the GitHub project page.